Affiliation

Abstract

Complex gene regulatory networks, not individual genes, control cellular function. Genes and gene products act together to determine cellular phenotypes. Estimation of these networks is necessary to understand cellular mechanisms, detect differences in gene regulation between cell types, and predict cellular response to interventions. A plethora of algorithms have been developed to infer network structure from experimental data. Here we provide a general introduction to the estimation of gene regulatory networks and the classes of proposed algorithms.

Conflict of interest statement

The author declares that he has no competing interests.

Figures

Figure 1

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A three gene network showing…

Figure 1

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A three gene network showing the different types of connectivity networks.

Figure 1

A three gene network showing the different types of connectivity networks.

Figure 2

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A five gene network where…

Figure 2

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A five gene network where nodes represent genes and edges represent positive-regulation (arrows)…

Figure 2

A five gene network where nodes represent genes and edges represent positive-regulation (arrows) or negative-regulation (squares). Note that this graph does not convey all of the necessary information – it is unclear whether expression of gene 2 requires expression of both genes 1 and 4 or whether either will suffice.

Figure 3

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A five gene Bayesian network…

Figure 3

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A five gene Bayesian network where nodes represent genes and edges represent regulatory…